Research Projects
I+D Projects
"Proyecto Para la Creacion de un servicio de informacion sobre Cartografia y Redes de Infraestructuras en la Comunidad Andaluza: Informatizacion de Cartografia y Redes en los Servicios de Aguas de Andalucia", Asociacion de Abastecimientos de Agua y Saneamientos de Andalucia (Ene.92/May.92), Inv.ppal. D. Carlos Gonzalez Spinola
"Modelacion del efecto de la irradiacion Laser sobre piel y sus implicaciones practicas en el tratamiento de tumores", Fundacion Antoni de Gimbernat, Cambrils, Tarragona-Espa¤a, Apr.95/Jul.95, Inv.ppal. O.Trelles
"Optimizacion y Paralelizacion de Software orientado a la prediccion de funcion en Proteinas", GlaxoWellcome S.A., Oct.98/Set.2000, Inv.ppal. O.Trelles
Data Mining and Multimedia (Query by Content in Scientific Videos)
Automatic tracking of moving bacterial cells in scientific videos
Rodriguez, A., Shotton D., Guil N. and Trelles O.
RIAO 2000, 6th Conference on "Content-Based multimedia information access
College de France, Paris, France, 2000
Automatic feature extraction in wound healing videos
Rodriguez, A., Shotton D., Trelles O. and Guil N.
RIAO 2000, 6th Conference on "Content-Based multimedia information access
College de France, Paris, France, 2000
Analysis and content-based querying of biological microscopy videos
Shotton D., Rodriguez, A., Guil N. and Trelles O.
15th International conference on Pattern Recognition
ICPR 2000 Barcelona, Spain 2000
Mining Low-level similarity signals from sequence databases
Rodriguez A., Thode G. Lopez D. and Trelles O.
High Performance Computers Applied to BioInformatics and
Computational Biology. 4th Conference on Systematics, cybernetics
and Informatics, SCI'2000
Orlando, Florida, USA 2000
Shotton,D.; Rodríguez, A.; Guil, N. and Trelles, O., "A metadata classification schema for semantic content analysis of videos", Journal of Microscopy (January 2002)
Rodríguez, A.; Shotton,D.; Guil, N. and Trelles, O., "Automatic analysis of the content of cell biological video and database organization of their metadata descriptors", IEEE-Multimedia transactions (in press)
Rodríguez, A.; Shotton,D.; Guil, N. and Trelles, O, "Analysis and Description of the Semantic Content of Cell Biological Videos", Multimedia Tools and Applications (in press)
Journals
O.Trelles, E.L.Zapata, J.M.Carazo (1994)
On an efficient parallelization of exhaustive sequence comparison algorithms
Computers Applications on BioSciences, CABIOS 10(5):509-511
O.Trelles, E.L.Zapata, J.Dopazo, A.W.F Coulson y J.M.Carazo (1994)
An Image processing approach to DotPlots : An X window-based program for interactive
analysis of dotplots derived from sequence and structural data
Computer Applications on BioSciences CABIOS (11), 3 pp.301-308
Ceron, C., Dopazo, J., Zapata, E.L., Carazo, J.M. and Trelles, O.
Parallel Implementation for DNAml Program on Message-Passing Architectures
Parallel Computing and Applications, vol 24 (5-6),June 98 pp.701-716
Trelles O., Andrade M.A., Valencia A., Zapata E.L., and Carazo J.M.
Computational Space Reduction and Parallelization of a new Clustering Approach for Large Groups of Sequences
BioInformatics vol.14 no.5 1998 (pp.439-451) (formerly CABIOS)
Trelles, O.; Ceron, C., Wang, H.C; Dopazo, and Carazo, J.M.
New phylogenetic venues opened by a novel implementation of the DNAml Algorithm
BioInformatics vol.14 no.6 1998 (pp.544-545) (formerly CABIOS)
Trelles O., (2000)
On the parallelisation of bioinformatic applications
Briefings in Bioinformatics (May, 2001) (vol.2) 2
PDF-file (.2MB)
C.O.S.Sorzano, J.M. Carazo and Trelles O., "Command line interfaces can be efficiently brought to graphics: COLIMATE (the COmmand LIne MATE) ",Software-Practice and Experience Vol: 32, Issue:9 (July 2002, pp:873-887)
Pérez A.J., Rodríguez, A., Trelles O., Thode G., "A computational strategy for protein function assignment which addresses the multidomain problem", Comparative and Functional Genomics , 2002, (3) pag.423-400
Jorge García de la Nava, Daniel Franco Santaella, Jesús Cuenca Alba, José María Carazo, Oswaldo Trelles, Alberto Pascual-Montano, "Engene: A web-based gene expression data processing and exploratory data analysis tool", Bioinformatics (in press, 2002)
Rodríguez, A.; Carazo, J.M. and A., Trelles O., "Mining Association Rules from Biological Databases", JASIS, Bioinformatics Special Issue (submitted)
Congress
Trelles, O., (1994), "Parallelization of Database Searching Algorithms for Biological Sequence Analysis" BRIDGE Advanced Practical Workshop on BioInformatics and its Role in Determining Biological Structures, March.94, CNB.Madrid-Spain,
Trelles, O., (1995), "Exhaustive Database Searching on the Cray T3D" Primera Reunion de la European Molecular Biology Network y la Red Tematica Nacional de BioComputacion. Oct.95, CNB.Madrid-Spain
Trelles, O. (1996), "Coarse-Grained Parallel Solutions for Sequence Analysis", (Invited Conference), First Workshop on High Performance Computing in BioMedicine, Sept.96 Santiago de Compostela, Espa¤a
Trelles, O., Zapata, E.L. and Carazo, J.M. (1994), "Mapping Strategies for Sequential Sequence Comparison Algorithms on LAN-based Message Passing Architectures", High Performace Computing and Networking (HPCN-Europe'94)
Marin, F.J., Trelles, O. and Sandoval, F., (1994), "Genetic Algorithms on LAN- Message Passing Architectures using PVM : Application to the Routing Problem", Parallel Program Solving from Nature (3th PPSN'94)
O.Trelles-Salazar, E.L.Zapata, J.Dopazo, A.W.F Coulson y J.M.Carazo (1994), "Exhaustive sequence database searching on the Cray-t3d", Genes, Proteins and Computers, Chester, U.K.
Carazo, J.M., Zapata, E.L. and Trelles, O., (1996), "Problemas Grand Challenge en Biologia y BioMedicina, su planteamiento y nuestros enfoques actuales", VII Jornadas de Paralelismo, Santiago de Compostela, Espa¤a
Biological Sequence Analysis: From Distributed to Distributed-Shared Memory Multiprocessors
Second Workshop on High Performance Computing in BioMedicine (Caceres, Espana, 1997)
Data Mining in Biological Sequence Databases: From 1D BioSequences to 3D structure.
Third Workshop on High Performance Computing in BioMedicine (Malaga, Espana, 1998)
Biological Sequence Analysis Area
Journals
E.Viguera, O.Trelles, J.L.Urdiales, J.M.Mates, F.Sanchez-Jimenez (1994)
Mammalian L-amino acid decarboxylases producing 1,4-diamines : Analogies among differences
Trends in Biochemical Sciences (TIBS) (1994)
Viguera E; Rodriguez A.; Hernandez P.; Krimer D.B., Trelles, O. and Schvartzman J.B.
A computer model for the analysis of DNA replication intermediates by two-dimensional agarose gel electrophoresis
Gene 217/1-2 (Sept.98) pp.41-49
Congress
Thode, G., Ranea, J.A., Alvarez, J.M and Trelles, O. (1994),
"A new analysis procedure to detect functional regions in protein sequences"
XXIX Jornadas de Genetica Luso-Espa¤olas Lleida, Spain
Thode, G., Ranea, J.A., Alvarez, J.M and Trelles, O. (1994)
"A new computer program to analyse protein sequences allows the localisation of interesting sites in the sequence of geminivirus genomes"
1st Internatonial Symposium on Geminiviruses, Almeria-Spain
Rodriguez, A., Viguera, E., Scharwzman, J.B, and Trelles O., (1995)
"Modelado del Analisis de la Replicacion del DNA por Electroferesis Bidimensional
en Geles de Agarosa"
I Jornadas de Informatica, Tenerife-Spain
Lasser/Tissue Interaction Modelling
Journals
M.A.Trelles, W.Verkruysse, O.Trelles, J.Sanchez and M.Velez.(1994)
"Enhancing Precision of Dermal Lesions Elimination by Laser"
Lasers in the Life Sciences 6(1)pp.1-10
Trelles, M.A., Verkruysse, W.; Pickering, J.W.; Trelles, O. and Mayayo, F.
"Purpura without vessel structure damage"
Dermatological Surgery-USA (in press)
Trelles, M.A, Verkruysse, W; Trelles, K.; Velez,M. y Trelles, O., (1995),
"Treatment of Benign pigmented lesions with 514 nm Argon Laser"
Oshiro's text book, Oshiro-Japan
Trelles, M.A., Coates, J.; Trelles,O., and Rigau,J.
"A preliminary study into the tissue interaction of the ultrapulse CO2 laser in cutaneous surgery"
Dermatologycal Surgery-USA (in press)
Trelles, M.A, Trelles, K., J.L.Cisneros and Trelles, O.,
"Soins Post- Operatoires aprŠs un resurfacing au laser"
Journal Med.Esth.et Chir.Derm. Vol.XXIII.90 Juin'96, 99-103
M.A. Trelles; L.Pardo; O. Trelles; M. Vélez; L.García-Solana; J.Rigau and J.J. Chamorro, "Clinical and Histological Effects of Facial Skin Rejuvenation with Pulsed- and Continuous-wave Flash-scanned CO2 Lasers", Aesthetic Surgery Journal (Sep-Oct, 2001) pp. 399-411
Congress
Rigau, J., Trelles, O. and Trelles, M.A. (1995)
"Ultrapulse laser resurfacing of wrinkles laboratory and clinics"
International Skin Peeling Symposium, Cannes
Trelles, M.A., Romero, L.F., Rodriguez, A. and Trelles, O. (1995)
New approach of CO2 laser use in plastic & dermo-cosmetic surgery
SPIE-Europto vol.2623. Proceedings of Medical Applications of Lasers III
pp.52-61, Barcelona-Spain,95
Romero, L.F., Rodriguez,A., Trelles, M.A. and Trelles, O. (1995)
Computational demands for laser/tissue interaction modelling
SPIE-Europto vol.2624.
Proceedings of Laser/Tissue Interaction in Tissue Optics, pp.33-40, Barcelona- Spain,95
Romero, L.F., Rodriguez,A., Trelles, M.A. and Trelles, O. (1996)
Efficient Computational Parallel Solutions for Laser/Tissue Interaction Modelling
BIOS-Europe'96, Viena, Austria
Trelles M.A and Trelles O., (1995)
Que hay de nuevo en laser-cirugia ?
XI Congreso Nacional de la Sociedad Espa¤ola de Medicina Estetica, Barcelona
Trelles O. and Trelles M.A., (1996)
Herramientas Computacionales de Visualizacion de la Accion del Laser sobre la Piel
XXXI Congreso de la Soc. Espa¤ola de Cirugia Plastica, Reparadora y Estetica, Madrid
Trelles, M.A. and Trelles, O. (1996)
Laser Resurfacing.Correlacion clinica con el laboratorio
XXXI Congreso de la Soc. Espa¤ola de Cirugia Plastica,
Reparadora y Estetica, Madrid, Spain
Trelles, M.A. and Trelles, O. (1996)
Tratamiento del envejecimiento cutaneo por laser, Evidencias clinicas
XXXI Congreso de la Soc. Espa¤ola de Cirugia
Plastica, Reparadora y Estetica Madrid, Espa¤a
Trelles, M.A. and Trelles, O. (1996)
Skin Rejuvenation by Laser
Laser Congress: At the dawn of the third millenium, Athenas (Greek Medical Laser
Association)
Using the Self Organising Tree Algorithm (SOTA), an unsupervised hierarchical neural network, to simultaneously classify and align protein sequences I Jornadas de Bioinformática, Cartagena, Spain, 14-16 Junio 2000
Automatic Analysis of Biological Scientific Videos, I Jornadas de Bioinformática, Cartagena, Spain, 14-16 Junio (2000)
"Estrategia para la asignación funcional de patrones peptídicos", I Jornadas de Bioinformática, Cartagena, Spain, 14-16 Junio (2000)
"Aplicación de extracción de reglas asociativas a bases de datos biológicas (Rodríguez, A., Carazo, J.M. y Trelles O.), II Jornadas de Bioinformática, Torremolinos, Málaga, España, 29 Mayo/1 de Junio (2001)
"Optimización de la asignación funcional de proteinas en base a los motivos del campo FT de la base de datos swissprot" (Perez, A.J., Thode, G. y Trelles, O.), II Jornadas de Bioinformática, Torremolinos, Málaga, España, 29 Mayo/1 de Junio (2001)
"Utilización del Algoritmo ANAGRAM en la definición de epítopos T en la cadena de la heteroglobina, un alergeno del Hamster Sirio" (J.Alvarez, A.J.Pérez, G.Thode, O.Trelles y M.Blanca), II Jornadas de Bioinformática, Torremolinos, Málaga, España, 29 Mayo/1 de Junio 2001
"Representación integral bi-dimensional de estructuras 3D" (J. García de la Nava, A. Rodríguez y O.Trelles), II Jornadas de Bioinformática, Torremolinos, Málaga, España, 29 Mayo/1 de Junio 2001
"Arquitectura para integrar el conocimiento biológico:una tarea en marcha", J.M. Fernández, M.M Roldán, O.Trelles y J.Aldana, II Jornadas de Bioinformática, Torremolinos, Málaga, España, 29 Mayo/1 de Junio 2001
"Comparación de estructuras 3D considerando los entornos de los aminoácidos" A.Rodríguez, N. Jimémez, J.M.Carazo y O.Trelles, II Jornadas de Bioinformática, Torremolinos, Málaga, España, 29 Mayo/1 de Junio 2001
"Nuevas redes neuronales auto-organizativas para el análisis y agrupamiento de patrones de expresión génica", Pascual, A.; Pérez, O., Trelles O.; Pascual-Marqui, R. y Carazo, J.M., II Jornadas de Bioinformática, Torremolinos, Málaga, España, 29 Mayo/1 de Junio 2001
"Extracción Automática de Conocimiento en Bases de Datos Biológicas", O.Trelles, XXIV Congreso Sociedad Española de Bioquímica y Biología Molecular, Valencia, 18-21 de Septiembre de 2001
"The use of Internet, Video and scanned 3D objects for our Natural History and Science Museums", Eduardo Ramírez, Per Djursvoll, Bjarne Meidell, Jan Erik Vold, Andrés Rodríguez and Oswaldo Trelles, 19th International Conference of ICOM (International Council of Museums) Barcelona, July, 1-6 2001
"Incorporation of biochemical knowledge in Geometric Hashing: statistical assessment", Jiménez-Lozano N, Rodríguez A, Chagoyen M., Pascual-Montano A, Trelles O, Carazo JM, Intelligent Systems for Molecular Biology, Edmonton, Canada, 2002
"Express-Fingerprints: a European consortium for the safety evaluation of new strains, including GMOs, of potential application in bio-processed food", Pierre Renault, Eric Guédon, Charlotte Barrière, Oscar Kuipers, Jan Kok, Sacha van Hijum, Philippe Bessières, Sébastien Girard, Oswaldo Trelles, Jorge Garcia de la Nava, Olga Perez, Eric Johansen, Kim Ib Soerensen, Anette Wind, François Gendre, Jerome Mengaud, Nathalie Goupil-Feuillerat, Celine Gobert.. Lactic Acid Bacteria Symposium, 1-5th September 2002 (NL). Neederlands, 2002
"Integración de bases de datos biológicas sobre la plataforma .NET", J.F. Aldana, M.M. Roldán, N. Moreno, M. Aguilera, I. Navas A.J.Pérez, J.García de la Nava, y O.Trelles, III Jornadas de Bioinformática, Salamanca, Spain, Septiembre, 16-18,2002
Protein Functional Assignment by using a Database of Hierarchized Keywords", Pérez, A.J, Thode, G., Rodríguez, A. and Trelles O., III Jornadas de Bioinformática, Salamanca, Spain, Septiembre, 16-18, 2002
"Engene: A gene expression data processing and exploratory data analysis tool", Oswaldo Trelles, Alberto Pascual-Montano, Jorge García de la Nava Ruiz, Jesús Cuenca, Daniel Franco Santaella, José-María Carazo, CNIO Meeting "DNA arrays 2002", Centro Nacional de Investigación Oncológica, 2002
Database Mediation: Beyond gene-expression clustering", J.F. Aldana, M. Roldán, M.M. Roldán, N. Moreno, I. Navas, A.J.Pérez, J.García de la Nava, and O.Trelles, 18th ACM Symposium on Applied Computing